Sequence comparisons between orthologous gene-rich regions of pepper and tomato. The green column on the left represents the tomato chromosome 2. A black dot on the top of the green column indicates the location of the centromere. The genetic location of each orthologous sequence pair was determined on the basis of the tomato genetic map (Tomato EXPEN-2000)  and is indicated by a red line on the green column. Pairs of horizontal bars represent the pepper (upper) and tomato (lower) sequences. Pepper clone names are presented on the right side of each sequence pair. Highly similar regions are depicted by black lines and inverted regions by red lines. Arrows indicate predicted genes and the number sets indicate the orthologous gene sets. Letters indicate genes that have no orthologous pairs. The colored boxes indicate transposable elements. The asterisks in the colored boxes indicate the transposons that the boundary is defined. The compared sequences show many highly syntenic regions, with many insertions in the pepper sequences. For detailed information on the compared BAC sequences, see Additional file 1 and 2.